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Author Topic: auxiliary.par and analysis pdb files with multiple frames?  (Read 2897 times)

Offline wwang02

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auxiliary.par and analysis pdb files with multiple frames?
« on: October 05, 2014, 04:55:54 pm »
1. I notice there are a bunch of data about DNA helixes in auxiliary.par. Does anyone know where I can find documents explaining what they are in detail, so that I can decide which is important to me.

2. Does anyone know how to analyze pdb files that contains multiple frames? I notice when 3DNA analyze those files, it only produce output for the first frame.

Offline xiangjun

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Re: auxiliary.par and analysis pdb files with multiple frames?
« Reply #1 on: October 06, 2014, 02:48:01 pm »
Quote
1. I notice there are a bunch of data about DNA helixes in auxiliary.par. Does anyone know where I can find documents explaining what they are in detail, so that I can decide which is important to me.
The auxiliary.par is meant to be auxiliary, and the meaning of each section should make more sense after you read x3dna_v1.5.pdf and tech_details.pdf distributed with 3DNA (in the $X3DNA/doc folder). If you have specific questions about a particular section, please post them here.

Quote
2. Does anyone know how to analyze pdb files that contains multiple frames? I notice when 3DNA analyze those files, it only produce output for the first frame.
You can try the Ruby script x3dna_ensemble in 3DNA v2.1. If you are performing analysis of DNA/RNA dynamics in MD simulations, you may find Rajendra Kumar's do_x3dna useful.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.